I would start with the Remote office DSL connection first. If your connections from office to office are public Internet connections that is most likely where your issue(s) begin.
By its very nature the public Internet is an uncontrolled resource. VoIP communication needs a controlled connection to be able to be a quality, reliable business communication tool. Otherwise you are at the mercy of public watering hole that has no care about what your company does for a living.
- Remote and Main office Internet connection bandwidth shaping. If you do not control usage currently then try to do so. Prioritize the VoIP communications over the other less time and packet critical items like ftp, web etc. This may be the trick that make your DSL connection reliable enough to be useful while still being cheap (in every sense of the term) enough for your business to use.
- The Main office Internet connection. Same as above.
- The Remote office DSL router. Some DSL routers choke above a certain point or are just not reliable. read up the model you have and evaluate whether or not you really like your current equipment.
- The Remote office VPN Router. Make sure the VPN router has the horsepower for the job. Make sure the firmware and model of the router match the task.
- The Main office VPN Router. Same as the Remote. Make sure the mfr, model, and type match the task. Even more so since the Main office may have more than one VPN connection.
Better yet, if budget allows, chuck any public connection and get a private connection. No matter what you do a VPN connection across the public Internet will always be a potential thorn in you VoIP communications. Your company may even classify a private connection (either leased line or virtual circuit) as secure enough to eliminate the VPN router. Though I doubt it.